Frederic Poitevin

Axel Levy, Gordon Wetzstein, Julien Martel et al.

Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule from millions of noisy and randomly oriented 2D projections in a computationally efficient manner, however, remains unsolved. Our method, cryoFIRE, performs ab initio heterogeneous reconstruction with unknown poses in an amortized framework, thereby avoiding the computationally expensive step of pose search while enabling the analysis of conformational heterogeneity. Poses and conformation are jointly estimated by an encoder while a physics-based decoder aggregates the images into an implicit neural representation of the conformational space. We show that our method can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy. We validate that the joint estimation of poses and conformations can be amortized over the size of the dataset. For the first time, we prove that an amortized method can extract interpretable dynamic information from experimental datasets.

Minseo Kim, Huanghao Mai, Jay Shenoy et al.

Generative models trained on public databases of protein structures, most of which have been determined by X-ray crystallography, now provide powerful priors for structure prediction. However, they are not readily conditioned on the measurements from a new crystallographic experiment, limiting their use for X-ray structure determination. In crystallography, the measured structure-factor amplitudes do not by themselves determine an electron density map or atomic structure because the associated phases are unobserved and must be inferred. Structure determination therefore remains an inverse problem in which candidate models must be both structurally plausible and consistent with measured diffraction data, often requiring substantial manual refinement by human experts. Emerging methods aim to incorporate experimental information more directly into predictive and refinement workflows. We present CrystalBoltz, a generative framework that casts crystallographic refinement as Bayesian inference over atomic structures and operates directly on structure-factor amplitudes. CrystalBoltz moves from unguided generation with a pre-trained prior over protein structures to experiment-guided posterior sampling, followed by atomic coordinate and B-factor refinement. Across multiple protein crystallography datasets, CrystalBoltz attains lower coordinate RMSD and lower R-factors than the strongest baselines considered, while reducing runtime by a factor of 33 relative to existing experimentally guided refinement.

Claire Donnat, Axel Levy, Frederic Poitevin et al.

Recent breakthroughs in high-resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology, chemistry, and pharmacological research. Recent next-generation volume reconstruction algorithms that combine generative modeling with end-to-end unsupervised deep learning techniques have shown promising preliminary results, but still face considerable technical and theoretical hurdles when applied to experimental cryo-EM images. In light of the proliferation of such methods, we propose here a critical review of recent advances in the field of deep generative modeling for cryo-EM volume reconstruction. The present review aims to (i) unify and compare these new methods using a consistent statistical framework, (ii) present them using a terminology familiar to machine learning researchers and computational biologists with no specific background in cryo-EM, and (iii) provide the necessary perspective on current advances to highlight their relative strengths and weaknesses, along with outstanding bottlenecks and avenues for improvements in the field. This review might also raise the interest of computer vision practitioners, as it highlights significant limits of deep generative models in low signal-to-noise regimes -- therefore emphasizing a need for new theoretical and methodological developments.

Youssef S. G. Nashed, Frederic Poitevin, Harshit Gupta et al.

Cryogenic electron microscopy (cryo-EM) provides images from different copies of the same biomolecule in arbitrary orientations. Here, we present an end-to-end unsupervised approach that learns individual particle orientations from cryo-EM data while reconstructing the average 3D map of the biomolecule, starting from a random initialization. The approach relies on an auto-encoder architecture where the latent space is explicitly interpreted as orientations used by the decoder to form an image according to the linear projection model. We evaluate our method on simulated data and show that it is able to reconstruct 3D particle maps from noisy- and CTF-corrupted 2D projection images of unknown particle orientations.